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Description
Is your feature request related to a problem?
As previously discussed #2630, #2651, etc... we probably don't want to be guessing by default if we can avoid it, particularly for elements where guess_types/elements (synonymous) is particularly error prone.
The ParmEdParser currently guesses by default elements if the atomic number doesn't match anything in Z2SYMB.
mdanalysis/package/MDAnalysis/topology/ParmEdParser.py
Lines 219 to 223 in b2b7bcb
| for z, name in zip(atomic_numbers, names): | |
| try: | |
| elements.append(Z2SYMB[z]) | |
| except KeyError: | |
| elements.append(guess_atom_element(name)) |
Describe the solution you'd like
Change the behaviour of the ParmeEdParser. If the element can't be found, then just assign the element as an empty string (as we do for the TOPParser).
Describe alternatives you've considered
Alternatively we could either: a) not assign elements if there's a bad element, or b) keep things as they are.
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